Ketogenic diets influence brain function and have been therapeutically used for anti-epileptic purposes. We investigated the effects of maternal ketogenic diets on the development of somatic and reflex responses in rat pups. These were born from mothers receiving: (i) normal fat (7%) + normal protein (17%); (ii) high-fat (55.4%) + normal protein; (iii) normal fat + low protein (8%); and (iv) high-fat + low protein (respectively, called N-17, K-17, N-8 and K-8). Ketogenic diets, but not the normal-fat diets, delayed the development of reflex and somatic responses. The effects were more evident when the ketogenic diet was associated with low protein content. The results suggest that fat excess can alter brain maturation, and this action is intensified by early protein-deficiency. Data raise concerns about the therapeutic use of ketogenic diets in newborn children.